Question: Transcriptome input for Sailfish tool
gravatar for andres.caballero
8 months ago by
andres.caballero0 wrote:

Hi there,

I would like to run the sailfish tool, but I can't find a reference transcriptome to map the reads and the sailfish tool doesn't have any built-in reference transcriptome. Would it be possible to add it? (human transcriptome) or else, where can I get it from to import it into my library? Thank you in advance.


ADD COMMENTlink modified 3 months ago by csm1650 • written 8 months ago by andres.caballero0
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson22k wrote:


There are no plans to include built-in reference transcriptome datasets at this time as these change and updated very quickly from the different data sources. Also, pairing between the reference transcriptome and the "File containing a mapping of transcripts to genes" inputs is critical for proper results.

Instead, obtain a set of reference mRNA reads (your "transcriptome") and the corresponding reference annotation (GTF or tabular format) from the same source at the same time. This ensures all the data will match correctly.

The RefSeq Genes track from UCSC is one choice.

Best, Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson22k
gravatar for csm165
3 months ago by
United States
csm1650 wrote:

Hello, Do you have any plans to change the interface for sailfish? Currently it says to either pick a genome from you history or use a built-in one, and if the genome you want isn't available to contact a galaxy admin. I'm sure you would save a bunch of people time and a bunch of emails to you guys if you made it clear that no built-in genomes will be available and/or remove that option.

Thanks, Chris

ADD COMMENTlink written 3 months ago by csm1650
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